[Bioperl-l] Problem with Bio::SeqIO opening gzipped files

[Jason Stajich]

When you pass in -file there is an implicit assumption that it is a
filename you are passing in, NOT a stream.

If you want to make this work, do this (you can replace 'zcat' with
'gunzip -c' if you prefer )
 open($fh, "zcat $filename.gz |");
 my $seqio  = new Bio::SeqIO(-fh => $fh, -format => 'genbank');

You can also provide multiple files in that zcat
 open($fh, "zcat $file1 $file2 ... |");

-jason
On Fri, 14 Nov 2003, Zayed  Albertyn wrote:

> Hi Andreas
>
> Adding the -c switch still doesnt work. I still get the same error
> message. Input is the full path to the file e.g.
>
> /cip0/db/GENBANK/RELEASE137/gbest13.seq.gz  == $path/$file
>
> I've written another script that does the normal
> open(FILE,"/bin/gunzip -c file1 |")
>
> and it works fine
>
> Z
>
> >
> >     my $seq_in = Bio::SeqIO::new(
> > 	'-file'   => "/bin/gunzip -c $path/$file|",
> > 	'-format' => 'genbank'
> >     );
> >
> >
> >
> > --
> > |()()|      Andreas Kähäri                                |(==)|
> > |)()(|      EMBL, European Bioinformatics Institute       |=)(=|
> > |()()|      Wellcome Trust Genome Campus, Hinxton         |(==)|
> > |)()(|      Cambridge, CB10 1SD                           |=)(=|
> > |()()|      United Kingdom                                |(==)|
> >
>
> -----------------------------------------------
> From: Zayed Albertyn
> Electric Genetics PTY Ltd
> Tel: +27 21 959 3645; Mobile: +2782 480 6097
> www.egenetics.com
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu